Coralline red algae (CRA) are key players in the construction and maintenance of biogenic reefs, and they have important functional roles in ecological systems in the Southwestern Atlantic (SWA). Like many other marine organisms, CRA are currently affected by global and local stressors, but little is known about their biodiversity and the environmental drivers that influence their distribution patterns in the SWA. In the present study, we quantified the species richness of CRA in six ecoregions within the SWA using DNA-based species delimitation methods. We then verified their distribution and identified the main drivers shaping the macroecological patterns of richness and β-diversity. We found 79 phylogenetic species that belong to the three main CRA orders (Sporolithales, Corallinales, and Hapalidiales), in the tropical and warm temperate SWA. Temperature, nutrients, and water current velocity were the main environmental drivers of CRAs in the evaluated ecoregions. The Eastern Brazil ecoregion stands out due to its high richness, exclusive species, β-diversity between ecoregions, and as a transitional zone of the SWA. The results of our study have several important practical implications with repercussions for monitoring actions and conservation planning for the coastal region. These results show that each ecoregion has unique characteristics, and the mesophotic habitat is of primary importance because it harbors species that are not found in other habitats, and because it provides structural connectivity with shallower habitats.